Comparison of predicted native structures of Met-enkephalin based on various accessible-surface-area solvent models.
We examine the variation and similarity of the native structures predicted from various accessible-surface-area solvent models for peptide Met-enkephalin. Both ECEPP/2 and ECEPP/3 force fields have been used in conjunction with ten different sets of accessible-surface-area parameterization. The native structures were determined by an implementation of the basin hopping Monte Carlo technique. The results suggest that the implicit solvent models examined in this study should be employed in computer simulations with extreme caution. In addition, the effect of fixing or not fixing the peptide angles omega has been examined. We conclude that fixing omega generally gives rise to a poor prediction.
Zhan
Lixin
L
Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada, N2L 3G1. lixinzhan@gmail.com
Chen
Jeff Z Y
JZ
Liu
Wing-Ki
WK
D003198:Computer Simulation; D004744:Enkephalin, Methionine / Q000737:chemistry*; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties
D012997:Solvents; D004744:Enkephalin, Methionine